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PDBsum entry 1gzm
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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
1gzm

 

 

 

 

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Contents
Protein chains
330 a.a. *
Ligands
NAG-NAG-BMA ×4
RET ×2
PLM ×4
PEF ×2
LDA ×3
C8E ×12
Metals
_ZN ×2
Waters ×40
* Residue conservation analysis
PDB id:
1gzm
Name: Signaling protein
Title: Structure of bovine rhodopsin in a trigonal crystal form
Structure: Rhodopsin. Chain: a, b. Other_details: disulfide link between a110 and a187, and b110 and b187
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: eye. Tissue: retina. Cell: rod photoreceptor
Biol. unit: Dimer (from PDB file)
Resolution:
2.65Å     R-factor:   0.202     R-free:   0.235
Authors: J.Li
Key ref:
J.Li et al. (2004). Structure of bovine rhodopsin in a trigonal crystal form. J Mol Biol, 343, 1409-1438. PubMed id: 15491621 DOI: 10.1016/j.jmb.2004.08.090
Date:
24-May-02     Release date:   20-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P02699  (OPSD_BOVIN) -  Rhodopsin from Bos taurus
Seq:
Struc: 		348 a.a.
329 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.jmb.2004.08.090 J Mol Biol 343:1409-1438 (2004)
PubMed id: 15491621  
 
 
Structure of bovine rhodopsin in a trigonal crystal form.
J.Li, P.C.Edwards, M.Burghammer, C.Villa, G.F.Schertler.
 
  ABSTRACT  
 
We have determined the structure of bovine rhodopsin at 2.65 A resolution using untwinned native crystals in the space group P3(1), by molecular replacement from the 2.8 A model (1F88) solved in space group P4(1). The new structure reveals mechanistically important details unresolved previously, which are considered in the membrane context by docking the structure into a cryo-electron microscopy map of 2D crystals. Kinks in the transmembrane helices facilitate inter-helical polar interactions. Ordered water molecules extend the hydrogen bonding networks, linking Trp265 in the retinal binding pocket to the NPxxY motif near the cytoplasmic boundary, and the Glu113 counterion for the protonated Schiff base to the extracellular surface. Glu113 forms a complex with a water molecule hydrogen bonded between its main chain and side-chain oxygen atoms. This can be expected to stabilise the salt-bridge with the protonated Schiff base linking the 11-cis-retinal to Lys296. The cytoplasmic ends of helices H5 and H6 have been extended by one turn. The G-protein interaction sites mapped to the cytoplasmic ends of H5 and H6 and a spiral extension of H5 are elevated above the bilayer. There is a surface cavity next to the conserved Glu134-Arg135 ion pair. The cytoplasmic loops have the highest temperature factors in the structure, indicative of their flexibility when not interacting with G protein or regulatory proteins. An ordered detergent molecule is seen wrapped around the kink in H6, stabilising the structure around the potential hinge in H6. These findings provide further explanation for the stability of the dark state structure. They support a mechanism for the activation, initiated by photo-isomerisation of the chromophore to its all-trans form, that involves pivoting movements of kinked helices, which, while maintaining hydrophobic contacts in the membrane interior, can be coupled to amplified translation of the helix ends near the membrane surfaces.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. A transmembrane slice showing H-bonding networks and hydrophobic contacts between the retinal-binding pocket and the cytoplasmic surface. 		Figure 6.
Figure 6. Environment of the 11-cis-retinal. (a) Environment of the protonated Schiff base and its counterion Glu113. (b) Environment of the ionone ring and the kinks in H6 and H7 cross-linked by a water molecule.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 1409-1438) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 2ydo 2ydv
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16941510 M.Domínguez, R.Alvarez, M.Pérez, K.Palczewski, and A.R.de Lera (2006).
The role of the 11-cis-retinal ring methyl substituents in visual pigment formation.
  Chembiochem, 7, 1815-1825.  
16906791 M.R.Lewis, and M.Kono (2006).
Rhodopsin deactivation is affected by mutations of Tyrl91.
  Photochem Photobiol, 82, 1442-1446.  
17103019 M.Y.Niv, L.Skrabanek, M.Filizola, and H.Weinstein (2006).
Modeling activated states of GPCRs: the rhodopsin template.
  J Comput Aided Mol Des, 20, 437-448.  
16597836 N.André, N.Cherouati, C.Prual, T.Steffan, G.Zeder-Lutz, T.Magnin, F.Pattus, H.Michel, R.Wagner, and C.Reinhart (2006).
Enhancing functional production of G protein-coupled receptors in Pichia pastoris to levels required for structural studies via a single expression screen.
  Protein Sci, 15, 1115-1126.  
16959786 O.Soubias, W.E.Teague, and K.Gawrisch (2006).
Evidence for specificity in lipid-rhodopsin interactions.
  J Biol Chem, 281, 33233-33241.  
16796383 P.H.Reggio (2006).
Computational methods in drug design: modeling G protein-coupled receptor monomers, dimers, and oligomers.
  AAPS J, 8, E322-E336.  
16731966 R.B.Jacobsen, K.L.Sale, M.J.Ayson, P.Novak, J.Hong, P.Lane, N.L.Wood, G.H.Kruppa, M.M.Young, and J.S.Schoeniger (2006).
Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry.
  Protein Sci, 15, 1303-1317.  
16777403 R.Grisshammer (2006).
Understanding recombinant expression of membrane proteins.
  Curr Opin Biotechnol, 17, 337-340.  
16972169 S.Kortagere, A.Roy, and E.L.Mehler (2006).
Ab initio computational modeling of long loops in G-protein coupled receptors.
  J Comput Aided Mol Des, 20, 427-436.  
16990262 S.R.Hawtin, J.Simms, M.Conner, Z.Lawson, R.A.Parslow, J.Trim, A.Sheppard, and M.Wheatley (2006).
Charged extracellular residues, conserved throughout a G-protein-coupled receptor family, are required for ligand binding, receptor activation, and cell-surface expression.
  J Biol Chem, 281, 38478-38488.  
16354660 S.Swift, A.J.Leger, J.Talavera, L.Zhang, A.Bohm, and A.Kuliopulos (2006).
Role of the PAR1 receptor 8th helix in signaling: the 7-8-1 receptor activation mechanism.
  J Biol Chem, 281, 4109-4116.  
16402913 T.W.Schwartz, T.M.Frimurer, B.Holst, M.M.Rosenkilde, and C.E.Elling (2006).
Molecular mechanism of 7TM receptor activation--a global toggle switch model.
  Annu Rev Pharmacol Toxicol, 46, 481-519.  
16928765 V.Soni, T.Yasui, E.Cahir-McFarland, and E.Kieff (2006).
LMP1 transmembrane domain 1 and 2 (TM1-2) FWLY mediates intermolecular interactions with TM3-6 to activate NF-kappaB.
  J Virol, 80, 10787-10793.  
16460808 V.V.Gurevich, and E.V.Gurevich (2006).
The structural basis of arrestin-mediated regulation of G-protein-coupled receptors.
  Pharmacol Ther, 110, 465-502.  
16799554 X.Yao, C.Parnot, X.Deupi, V.R.Ratnala, G.Swaminath, D.Farrens, and B.Kobilka (2006).
Coupling ligand structure to specific conformational switches in the beta2-adrenoceptor.
  Nat Chem Biol, 2, 417-422.  
17098868 X.Zhao, Y.Nagai, P.J.Reeves, P.Kiley, H.G.Khorana, and S.Zhang (2006).
Designer short peptide surfactants stabilize G protein-coupled receptor bovine rhodopsin.
  Proc Natl Acad Sci U S A, 103, 17707-17712.  
17176053 Y.Choi, and J.B.Konopka (2006).
Accessibility of cysteine residues substituted into the cytoplasmic regions of the alpha-factor receptor identifies the intracellular residues that are available for G protein interaction.
  Biochemistry, 45, 15310-15317.  
16408006 A.Jongejan, M.Bruysters, J.A.Ballesteros, E.Haaksma, R.A.Bakker, L.Pardo, and R.Leurs (2005).
Linking agonist binding to histamine H1 receptor activation.
  Nat Chem Biol, 1, 98.  
15952243 A.Jongejan, and R.Leurs (2005).
Delineation of receptor-ligand interactions at the human histamine H1 receptor by a combined approach of site-directed mutagenesis and computational techniques - or - how to bind the H1 receptor.
  Arch Pharm (Weinheim), 338, 248-259.  
15572356 B.Li, N.M.Nowak, S.K.Kim, K.A.Jacobson, A.Bagheri, C.Schmidt, and J.Wess (2005).
Random mutagenesis of the M3 muscarinic acetylcholine receptor expressed in yeast: identification of second-site mutations that restore function to a coupling-deficient mutant M3 receptor.
  J Biol Chem, 280, 5664-5675.
PDB code: 2amk
16154351 B.Zheng, C.J.Gerdts, and R.F.Ismagilov (2005).
Using nanoliter plugs in microfluidics to facilitate and understand protein crystallization.
  Curr Opin Struct Biol, 15, 548-555.  
15626708 C.J.daCosta, D.E.Kaiser, and J.E.Baenziger (2005).
Role of glycosylation and membrane environment in nicotinic acetylcholine receptor stability.
  Biophys J, 88, 1755-1764.  
16168633 C.Riekel, M.Burghammer, and G.Schertler (2005).
Protein crystallography microdiffraction.
  Curr Opin Struct Biol, 15, 556-562.  
16126723 E.Hamelin, C.Thériault, G.Laroche, and J.L.Parent (2005).
The intracellular trafficking of the G protein-coupled receptor TPbeta depends on a direct interaction with Rab11.
  J Biol Chem, 280, 36195-36205.  
15722344 E.Urizar, S.Claeysen, X.Deupí, C.Govaerts, S.Costagliola, G.Vassart, and L.Pardo (2005).
An activation switch in the rhodopsin family of G protein-coupled receptors: the thyrotropin receptor.
  J Biol Chem, 280, 17135-17141.  
15786429 F.Blomgren, and S.Larsson (2005).
Exploring the potential energy surface of retinal, a comparison of the performance of different methods.
  J Comput Chem, 26, 738-742.  
16027155 F.J.Bartl, O.Fritze, E.Ritter, R.Herrmann, V.Kuksa, K.Palczewski, K.P.Hofmann, and O.P.Ernst (2005).
Partial agonism in a G Protein-coupled receptor: role of the retinal ring structure in rhodopsin activation.
  J Biol Chem, 280, 34259-34267.  
16218991 G.V.Nikiforovich, B.Mihalik, K.J.Catt, and G.R.Marshall (2005).
Molecular mechanisms of constitutive activity: mutations at position 111 of the angiotensin AT1 receptor.
  J Pept Res, 66, 236-248.  
16199504 G.V.Nikiforovich, and G.R.Marshall (2005).
Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor.
  Biophys J, 89, 3780-3789.  
16114870 I.D.Pogozheva, B.X.Chai, A.L.Lomize, T.M.Fong, D.H.Weinberg, R.P.Nargund, M.W.Mulholland, I.Gantz, and H.I.Mosberg (2005).
Interactions of human melanocortin 4 receptor with nonpeptide and peptide agonists.
  Biochemistry, 44, 11329-11341.
PDB codes: 2iqp 2iqr 2iqs 2iqu
16353922 I.D.Pogozheva, M.J.Przydzial, and H.I.Mosberg (2005).
Homology modeling of opioid receptor-ligand complexes using experimental constraints.
  AAPS J, 7, E434-E448.  
15889287 J.Ciarkowski, M.Witt, and R.Slusarz (2005).
A hypothesis for GPCR activation.
  J Mol Model, 11, 407-415.  
15979374 J.Y.Springael, E.Urizar, and M.Parmentier (2005).
Dimerization of chemokine receptors and its functional consequences.
  Cytokine Growth Factor Rev, 16, 611-623.  
16218993 M.J.Przydzial, I.D.Pogozheva, J.C.Ho, K.E.Bosse, E.Sawyer, J.R.Traynor, and H.I.Mosberg (2005).
Design of high affinity cyclic pentapeptide ligands for kappa-opioid receptors.
  J Pept Res, 66, 255-262.  
16041481 N.G.Abdulaev, C.Zhang, A.Dinh, T.Ngo, P.N.Bryan, D.M.Brabazon, J.P.Marino, and K.D.Ridge (2005).
Bacterial expression and one-step purification of an isotope-labeled heterotrimeric G-protein alpha-subunit.
  J Biomol NMR, 32, 31-40.  
16129667 N.G.Abdulaev, T.Ngo, C.Zhang, A.Dinh, D.M.Brabazon, K.D.Ridge, and J.P.Marino (2005).
Heterotrimeric G-protein alpha-subunit adopts a "preactivated" conformation when associated with betagamma-subunits.
  J Biol Chem, 280, 38071-38080.  
15952240 R.E.Stenkamp, D.C.Teller, and K.Palczewski (2005).
Rhodopsin: a structural primer for G-protein coupled receptors.
  Arch Pharm (Weinheim), 338, 209-216.  
15928919 S.Filipek (2005).
Organization of rhodopsin molecules in native membranes of rod cells--an old theoretical model compared to new experimental data.
  J Mol Model, 11, 385-391.  
16093246 S.J.Han, F.F.Hamdan, S.K.Kim, K.A.Jacobson, L.M.Bloodworth, B.Li, and J.Wess (2005).
Identification of an agonist-induced conformational change occurring adjacent to the ligand-binding pocket of the M(3) muscarinic acetylcholine receptor.
  J Biol Chem, 280, 34849-34858.  
16339447 V.M.Tesmer, T.Kawano, A.Shankaranarayanan, T.Kozasa, and J.J.Tesmer (2005).
Snapshot of activated G proteins at the membrane: the Galphaq-GRK2-Gbetagamma complex.
  Science, 310, 1686-1690.
PDB code: 2bcj
16331961 W.Xu, M.Campillo, L.Pardo, J.Kim de Riel, and L.Y.Liu-Chen (2005).
The seventh transmembrane domains of the delta and kappa opioid receptors have different accessibility patterns and interhelical interactions.
  Biochemistry, 44, 16014-16025.  
15475355 J.M.Janz, and D.L.Farrens (2004).
Role of the retinal hydrogen bond network in rhodopsin Schiff base stability and hydrolysis.
  J Biol Chem, 279, 55886-55894.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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